Database-assisted global metabolomics profiling of pleural effusion induced by tuberculosis and malignancy

Database-assisted global metabolomics has received growing attention due to its capability for unbiased identification of metabolites in various biological samples. Herein, we established a mass spectrometry (MS)-based database-assisted global metabolomics method and investigated metabolic distance between pleural effusion induced by tuberculosis and malignancy, which are difficult to be distinguished due to their similar clinical symptoms. The present method utilized a liquid chromatography (LC) system coupled with high resolution mass spectrometry (MS) working on full scan and data dependent mode for data acquisition. Unbiased identification of metabolites was performed through mass spectral searching and then confirmed by using authentic standards. As a result, a total of 194 endogenous metabolites were identified and 33 metabolites were found to be differentiated between tuberculous and malignant pleural effusions. These metabolites involved in tryptophan catabolism, bile acid biosynthesis, and β-oxidation of fatty acids, provided non-invasive biomarkers for differentiation of the pleural effusion samples with high sensitivity and specificity.     

非衍生化高效液相色谱-串联质谱法快速检测生物体液中草甘膦、草铵膦及代谢物

建立了一种非衍生化高效液相色谱-串联质谱快速检测生物体液中草甘膦、草铵膦及其代谢物等8种极性农药的方法。8种极性农药经Metrosep A Supp 5阴离子色谱柱(150 mm×4.0 mm,5μm)分离,以纯水-200 mmol/L碳酸氢铵溶液(含0.1%氨水)为流动相进行梯度洗脱,负离子多反应监测(MRM)模式进行检测。实验结果表明,8种极性农药在0.5~50 ng/mL范围内线性关系良好(r²>0.99),检出限(S/N≥3)为0.08~0.3 ng/mL,定量下限(S/N≥10)为0.3~1 ng/mL。方法的基质效应为86.5%~106%,目标化合物的回收率为81.5%~114%,日内相对标准偏差(RSD)为0.30%~2.8%,日间RSD为0.50%~5.3%。该方法无需复杂的衍生化过程,简便快速、灵敏度高、稳定性好,适用于生物体液中8种极性农药的检测。     

A paradigm shift in rate determining step from single electron transfer between phenylsulfinylacetic acids and iron(III) polypyridyl complexes to nucleophilic attack of water to the produced sulfoxide radical cation: a non‐linear Hammett

Mechanism of oxidative decarboxylation of phenylsulfinylacetic acids (PSAAs) by iron(III) polypyridyl complexes in aqueous acetonitrile medium has been investigated spectrophotometrically. An initial intermediate formation between PSAA and [Fe(NN)₃]³⁺ is confirmed from the observed Michaelis–Menten kinetics and fractional order dependence on PSAA. Significant rate retardation with concentration of [Fe(NN)₃]³⁺ is rationalized on the basis of coordination of a water molecule at the carbon atom adjacent to the ring nitrogen of the metal polypyridyl complexes by nucleophilic attack at higher concentrations. Electron‐withdrawing and electron‐releasing substituents in PSAA facilitate the reaction and Hammett correlation gives an upward ‘V’ shaped curve. The apparent upward curvature is rationalized based on the change in the rate determining step from electron transfer to nucleophilic attack, by changing the substituents from electron‐releasing to electron‐withdrawing groups. Electron‐releasing substituents in PSAA accelerate the electron transfer from PSAA to the complex and also stabilize the intermediate through resonance interaction leading to negative reaction constants (ρ). Conversely, electron‐withdrawing groups, while retarding the electron transfer exert an accelerating effect on the nucleophilic attack of H₂O which leading to low magnitude of ρ⁺ compared to high ρ^? values of electron‐releasing groups. Marcus theory is applied, and a fair agreement is seen with the experimental values. Copyright © 2016 John Wiley & Sons, Ltd.     

Quantum Zeno dynamics in atoms and cavities

Quantum Zeno Dynamics restricts the evolution of a system in a tailorable subspace of the Hilbert space by repeated measurements of a proper observable. This restricted dynamics can be counterintuitive and lead to the generation of interesting nonclassical states. We describe an experiment implementing the Zeno dynamics in an atomic Rydberg level manifold, and we propose an implementation in the cavity quantum electrodynamics context. Both systems open promising perspectives for quantum-enabled metrology and decoherence studies.     

基于非靶向代谢组学的茄梨和红茄梨成熟期果皮代谢产物的差异分析

为了探究西洋梨品种茄梨及其红色芽变红茄梨成熟期果皮代谢产物差异,采用超高效液相色谱-质谱联用技术,对茄梨和红茄梨成熟期果皮进行非靶向代谢组学研究。通过主成分分析和正交偏最小二乘判别分析,构建了多变量统计分析模型,结合模型和变量重要性投影与最大差异倍数值,基于精确质量数、二级碎片以及同位素分布,使用PMDB(Plant Metabolome Database)数据库进行定性,筛选并鉴定出茄梨和红茄梨果皮中显著性变化(P<0.05, VIP(variable importance in project)≥1)的差异代谢物有83种,主要包括酚酸类、黄酮类和氨基酸类物质,涉及类黄酮代谢、氨基酸代谢、苯丙烷类代谢等代谢途径,其中53种物质含量上调,30种物质表达下调。通过KEGG(Kyoto Encyclopedia of Genes and Genomes)数据库进一步对差异代谢物质进行通路富集分析,差异代谢物主要分布在20条代谢途径中,P<0.05的代谢途径有6条,分别是类黄酮生物合成、黄酮和黄酮醇生物合成、苯丙烷生物合成、丁酸酯代谢、苯丙氨酸代谢、酪氨酸代谢。这些差异代谢物的变化可能是导致茄梨和红茄梨果皮色泽不同的原因。该研究从植物代谢组学角度初步揭示了茄梨和红茄梨成熟期果皮的代谢产物差异性。     

Characteristics of Friedel pairs and diffraction contrast tomography with non‐perpendicular rotation axis

The characteristics of Friedel pairs in diffraction contrast tomography (DCT) are studied in the condition that the rotation axis of the sample is not exactly perpendicular to the incident X‐ray direction. For the rotation axis approximately aligned along the vertical direction, the Friedel pairs close to the horizontal plane are insensitive to the non‐perpendicularity of the rotation axis, and can be used to refine the sample‐to‐detector distance and X‐ray energy, while the Friedel pairs close to the vertical direction are sensitive to the non‐perpendicularity of the rotation axis, and can be used to determine the rotation axis orientation. The correct matching proportion of Friedel pairs decreases with increasing non‐perpendicularity of the rotation axis. A method of data processing considering rotation axis misalignment is proposed, which significantly increases the correct matching and indexing proportions of the diffraction spots. A pure aluminium polycrystalline sample is investigated using DCT at beamline 4W1A of Beijing Synchrotron Radiation Facility. Based on the analysis of Friedel pairs, the sample‐to‐detector distance and X‐ray energy are refined to be 8.67 mm and 20.04 keV, respectively. The non‐perpendicular angle of the rotation axis is calculated to be 0.10°. With these refined geometric parameters, the matching proportion of the spatial position of diffraction spots is 90.62%. Three‐dimensional reconstruction of the sample with 13 grains is realised using the algebraic reconstruction technique. It is demonstrated that the precise correction of the orientation of the sample rotation axis is effective in DCT suffering from rotation axis misalignment, and the higher accuracy in determining the rotation axis is expected to improve the reconstruction precision of grains.     

An efficient splitting technique for two‐layer shallow‐water model

We consider the numerical approximation of the weak solutions of the two‐layer shallow‐water equations. The model under consideration is made of two usual one‐layer shallow‐water model coupled by nonconservative products. Because of the nonconservative products of the system, which couple both one‐layer shallow‐water subsystems, the usual numerical methods have to consider the full model. Of course, uncoupled numerical techniques, just involving finite volume schemes for the basic shallow‐water equations, are very attractive since they are very easy to implement and they are costless. Recently, a stable layer splitting technique was introduced [Bouchut and Morales de Luna, M2AN Math Model Numer Anal 42 (2008), 683–698]. In the same spirit, we exhibit new splitting technique, which is proved to be well balanced and non‐negative preserving. The main benefit issuing from the here derived uncoupled method is the ability to correctly approximate the solution of very severe benchmarks. © 2014 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 31: 1396–1423, 2015     

Non-linear couplings,from the early to the late time universe

Deciphering the mechanisms at play in the formation and evolution of the large-scale structure of the universe is part of the scientific goals of many projects of observational cosmology. In particular, large-scale structure observations can be used to infer mode-coupling effects, whether they come from the physics of the early universe or from its late time evolution. Specificities of such couplings are presented, noting that in principle they can be directly detected through bispectra of the cosmic microwave background temperature anisotropies or density in the local universe. The existence of such couplings have however more far-reaching consequences for the growth of the structure. Those are sketched as well as their possible observational impacts.     

Comparison of the activation time effects and the internal energy distributions for the CID,PQD and HCD excitation modes

Reproducibility among different types of excitation modes is a major bottleneck in the field of tandem mass spectrometry library development in metabolomics. In this study, we specifically evaluated the influence of collision voltage and activation time parameters on tandem mass spectrometry spectra for various excitation modes [collision‐induced dissociation (CID), pulsed Q dissociation (PQD) and higher‐energy collision dissociation (HCD)] of Orbitrap‐based instruments. For this purpose, internal energy deposition was probed using an approach based on Rice–Rampserger–Kassel–Marcus modeling with three thermometer compounds of different degree of freedom (69, 228 and 420) and a thermal model. This model treats consecutively the activation and decomposition steps, and the survival precursor ion populations are characterized by truncated Maxwell–Boltzmann internal energy distributions. This study demonstrates that the activation time has a significant impact on MS/MS spectra using the CID and PQD modes. The proposed model seems suitable to describe the multiple collision regime in the PQD and HCD modes. Linear relationships between mean internal energy and collision voltage are shown for the latter modes and the three thermometer molecules. These results suggest that a calibration based on the collision voltage should provide reproducible for PQD, HCD to be compared with CID in tandem in space instruments. However, an important signal loss is observed in PQD excitation mode whatever the mass of the studied compounds, which may affect not only parent ions but also fragment ions depending on the fragmentation parameters. A calibration approach for the CID mode based on the variation of activation time parameter is more appropriate than one based on collision voltage. In fact, the activation time parameter in CID induces a modification of the collisional regime and thus helps control the orientation of the fragmentation pathways (competitive or consecutive dissociations). Copyright © 2014 John Wiley & Sons, Ltd.     

Profiling of grape monoterpene glycosides (aroma precursors) by ultra‐high performance‐liquid chromatography‐high resolution mass spectrometry (UHPLC/QTOF)

A ‘suspect screening analysis’ method for grape metabolomics by ultra‐high performance‐liquid chromatography (UHPLC) and high‐resolution quadrupole‐time of flight (QTOF) mass spectrometry was recently developed. This method was applied to study grape monoterpene glycosides, the main grape aroma precursors. Since standard compounds were not available, they were tentatively identified by overlapping various analytical approaches, in agreement with the indications recommended in mass spectrometry (MS)‐based metabolomics. Accurate mass and isotopic pattern, MS/MS fragmentation, correlation between fragments observed and putative structures and between liquid chromatography coupled with mass spectrometry (LC/MS) and gas chromatography/mass spectrometry signals were studied. Seventeen monoterpene glycosides were identified without performing the hydrolytic artifacts commonly used to study these compounds which may affect sample profile. This is the first time that a detailed study of these aroma precursors has been carried out by direct LC/MS analysis. Copyright © 2014 John Wiley & Sons, Ltd.